The aim of the present study was to propose and validate FAST3D: a fully automatic three-dimensional (3D) assessment of the surgical accuracy and the long-term skeletal stability of orthognathic surgery. To validate FAST3D, the agreement between FAST3D and a validated state-of-the-art semi-automatic method was calculated by intra-class correlation coefficients (ICC) at a 95 % confidence interval. A one-sided hypothesis test was performed to evaluate whether the absolute discrepancy between the measurements produced by the two methods was statistically significantly below a clinically relevant error margin of 0.5 mm. Ten subjects (six male, four female; mean age 24.4 years), class II and III, who underwent a combined three-piece Le Fort I osteotomy, bilateral sagittal split osteotomy and genioplasty, were included in the validation study. The agreement between the two methods was excellent for all measurements, ICC range (0.85-1.00), and fair for the rotational stability of the chin, ICC = 0.54. The absolute discrepancy for all measurements was statistically significantly lower than the clinical relevant error margin (p < 0.008). Within the limitations of the present validation study, FAST3D demonstrated to be reliable and may be adopted whenever appropriate in order to reduce the work load of the medical staff.